Frans J. de Bruijn, PhD, was Director of the Laboratory for Plant-Microbe Interactions and Environment, a mixed INRAE/CNRS research facility with about 100 scientists and support staff in Toulouse, France. He is presently Director of Recherche DR1 and editor of multiple books on a variety of topics.

Hauke Schmidt, PhD, is a member of the management team at the National BE-Basic Program and Senior Scientist and Theme Council member at TI Food & Nutrition.

Luca S. Cocolin is Full Professor in the Department of Agricultural, Forest, and Food Sciences at the University of Torino, Italy.

Michael Sauer is Assistant Professor at the Department of Biotechnology of BOKU-University of Natural Resources and Life Sciences in Vienna, Austria.

David Dowling, PhD, co-founded MicroGen Biotechnology Limited and is the Head of the Faculty of Science at the Institute of Technology Carlow.

Linda Thomashow, PhD, Research Geneticist at the USDA Agricultural Research Service's Wheat Health, Genetics and Quality Research Unit and Professor in Plant Pathology and Molecular Plant Sciences at Washington State University, USA.

Preface xxi List of Contributors xxii Acknowledgments xxviii Introduction xxix Section 1 Good Microbes in Medicine 1
Co-Edited by Hauke Smidt and Frans J. de Bruijn Chapter 1 Modern Medicine Relies on the Help of Microorganisms - From Vaccine Production to Cancer Medication 3Letícia Parizotto, Larissa Brumano, Eduardo Kleingesinds, and Adalberto Pessoa Junior 1.1 Introduction: Good Microorganisms and Our Health 3 1.2 Bad Microorganisms: Epidemics Boosted Modern Medicine 4 1.3 Antimicrobial Peptides: A New Therapeutic Alternative to Antibiotics? 4 1.4 Microorganisms as Tools: Recombinant DNA Technology (rDNAT) 5 1.5 Vaccines: The Use of Microorganisms in the Frontline against Diseases 7 1.6 Anticancer Drugs: Many Ways to Fight Cancer with Good Microorganisms 8 1.7 Gene Therapy: The Future of Modern Medicine 9 1.8 Concluding Remarks and Perspectives 10 Acknowledgments 10 Chapter 2 How Nursing Mothers Protect Their Babies with Bifidobacteria 13Nick M. Jensen, Britta E. Heiss, and David A. Mills 2.1 Bifidobacterium Species and Diversity 13 2.2 Human Milk Oligosaccharides 14 2.3 Bifidobacterial Metabolism 14 2.4 Benefits of Bifidobacterium 15 2.5 Global Distribution of Bifidobacterium 16 2.6 Supporting Persistent Bifidobacterium Populations 16 2.7 Summary 18 Acknowledgments 18 Chapter 3 Gut Microbiome and the Immune System: Role in Vaccine Response 22Helena Ipe Pinheiro Guimaraes, Jorgen De Jonge, Debbie Van Baarle, and Susana Fuentes 3.1 Immunology of Vaccines 22 3.1.1 Induction of Protective Immunity by Vaccination 22 3.1.2 Evolution of Vaccines 23 3.1.3 Vaccine Limitations 24 3.2 Gut Microbiome and the Immune System 24 3.2.1 Microbiome Development in Life 24 3.2.2 Host-microbe Interactions: Impact on Health 25 3.3 Microbiome and Vaccine Response 27 3.3.1 Mechanistic Studies in Animal Models 27 3.4 Role of the Microbiome in Vaccine Response in Human Studies 28 3.5 Conclusions and Future Perspectives 29 Chapter 4 Probiotics for Prevention or Treatment of Food Allergies 35Agnes S. Y. Leung, Wenyin Loh, and Mimi L. K. Tang 4.1 Introduction 35 4.2 Prevention of Food Allergy 36 4.3 Treatment of Food Allergy 37 4.3.1 Clinical Use of Probiotics in Food Immunotherapy 38 4.3.2 Preclinical Studies of the Effects of Probiotics for Treatment of Food Allergy 39 4.4 Conclusion 39 Chapter 5 COVID-19, Microbiota, and Probiotics 43Marta Mozota, Leónides Fernández, and Juan Miguel Rodríguez 5.1 Introduction 43 5.2 Relationship between COVID-19 and the Microbiota 44 5.3 Respiratory Microbiota in Patients with COVID-19 45 5.4 Gut Microbiota in Patients with COVID-19 45 5.5 Probiotics and COVID-19 46 Chapter 6 Underarm Body Odor, the Microbiome, and Probiotic Treatment 52Britta De Pessemier, Rune Daneels, Tom Van De Wiele, and Chris Callewaert 6.1 Skin Structure and Function 52 6.2 Sweat 52 6.2.1 Sweat Glands 6.2.1.1 Eccrine Glands 53 6.2.1.2 Apocrine Glands 53 6.2.1.3 Apoeccrine Glands 53 6.2.1.4 Sebaceous Glands 54 6.3 Skin and Underarm Microbiome 54 6.4 Axillary Microbiome 54 6.5 Bromhidrosis Pathophysiology 56 6.5.1 Steroid-based Malodor 56 6.5.2 Long-chain Fatty Acids (LCFAs) 56 6.5.3 VFA-based Malodor 57 6.5.4 Thioalcohol-based Malodor 57 6.6 Methods to Treat Body Odor 57 6.6.1 Conventional Methods 57 6.6.1.1 Deodorants 57 6.6.1.2 Antiperspirants 58 6.6.1.3 Antibiotics 58 6.6.1.4 Medication 58 6.6.1.5 Botox 58 6.6.1.6 Surgery 58 6.6.2 Alternative Methods 58 6.6.2.1 Pre-, Pro-, and Postbiotics 59 6.6.2.2 Armpit Bacterial Transplant 60 6.6.2.3 Bacteriotherapy 60 6.7 Conclusions 60 Acknowledgments 61 Chapter 7 The Enigma of Prevotella copri 64Petia Kovatcheva-Datchary 7.1 Introduction 64 7.2 Prevotella copri Physiology, Growth, and Metabolism 64 7.3 Prevotella copri, an Important Member of the Human Gut Microbiota 65 7.4 The Unexplored Diversity of Prevotella copri 65 Chapter 8 Future Perspectives of Probiotics and Prebiotics in Foods and Food Supplements 69Z. H. Hassan, F. Hugenholtz, E. G. Zoetendal, and Hauke Smidt 8.1 Introduction 69 8.2 Function of the GI Tract Microbiota 71 8.3 Modulating the GI Tract Microbiota to Improve Health 71 8.3.1 Modulating the GI Tract Microbiota with Probiotics 72 8.3.2 Criteria for a Microorganism to Be Classified as Probiotic 72 8.4 Modulating the GI Tract Microbiota with Prebiotics 73 8.5 Modulating the GI Tract Microbiota with Synbiotics 74 8.6 Future Perspectives 76 8.6.1 Next Generation Probiotics 78 8.6.2 Next Generation Prebiotics 80 Acknowledgments 82 Section 2 Good Microbes in Food Production 89Co-Edited by Luca S. Cocolin and Frans J. de Bruijn Chapter 9 Bioprotective Cultures and Bacteriocins for Food 91Sara Arbulu, Beatriz Gómez-Sala, Enriqueta Garcia-Gutierrez,
and Paul D. Cotter 9.1 Introduction 91 9.1.1 Food Safety Hazards 91 9.1.2 Bioprotection: Fermentation, Protective Cultures, and Bacteriocins 92 9.1.3 Fermented Foods 92 9.1.4 Protective Cultures 92 9.1.5 Bacteriocins 92 9.1.6 Bacteriocin Classification 92 9.2 Bioprotection of Milk and Dairy Products 93 9.2.1 Milk Products and Their Importance in Society 93 9.2.2 Spoilage and Food-borne Pathogenic Bacteria in Milk and Dairy Products 93 9.3 Fermented Dairy Products 93 9.4 Application of Bacteriocins and Their Protective Cultures in Milk and Dairy Products 94 9.5 Bioprotection of Meat and Meat Products 95 9.5.1 Meat and Meat Products and Their Importance in Society 95 9.5.2 Spoilage and Food-borne Pathogenic Bacteria in Meat and Meat Products 95 9.6 Fermented Meat Products 95 9.7 Application of Protective Cultures and Their Bacteriocins in Meat and Meat Products 96 9.8 Bioprotection of Fresh Fish and Fish Products 97 9.8.1 Fish and Fish Products and Their Importance in Society 97 9.8.2 Spoilage and Food-borne Pathogenic Bacteria in Fish and Fish Products 97 9.9 Fermented Fish Products 98 9.10 Application of Protective Cultures and Their Bacteriocins in Fish and Fish Products 100 9.11 Bioprotection of Fruits and Vegetables 100 9.11.1 Fruit and Vegetables and Their Importance in Society 100 9.11.2 Spoilage and Pathogenic Bacteria in Fruit and Vegetables 103 9.12 Fermented Fruits and Vegetables Products 103 9.13 Application of Protective Cultures and Their Bacteriocins in Fruit, Vegetables, and By-products 104 9.14 Regulatory Issues in Bioprotection 104 9.15 Conclusions 106 Acknowledgments 106 Chapter 10 Aromatic Yeasts: Revealing Their Flavor Potential in Food Fermentations 113Amparo Gamero, Mónica Flores, and Carmela Belloch 10.1 Introduction 113 10.2 Yeast Aroma in Alcoholic Beverages 113 10.2.1 Yeast: Saccharomyces and Non-Saccharomyces 114 10.2.2 Aromatic Precursors 115 10.2.3 Fermentative Aroma Compounds 116 10.3 Yeast Aroma in Foods from Animal Sources 116 10.3.1 Yeast: Debaryomyces and Kluyveromyces 117 10.3.2 Fermentation Aroma Compounds 117 10.4 Yeast Aroma in Other Fermentations 120 10.4.1 Vegetables 121 10.4.2 Traditional Fermentations 122 10.5 Final Remarks 125 Acknowledgments 125 Chapter 11 Beneficial Microbiota in Ethnic Fermented Foods and Beverages 130Jyoti Prakash Tamang and Namrata Thapa 11.1 Introduction 130 11.2 Ethnic Fermented Foods 130 11.3 Diversity of Beneficial Microorganisms in Ethnic Fermented Foods 132 11.3.1 Lactic Acid Bacteria 133 11.3.2 Non-Lactic Acid Bacteria 134 11.3.3 Yeasts 135 11.3.4 Filamentous Molds 135 11.3.5 Probiotic Strains from Ethnic Fermented Foods 136 11.3.6 Functional Profiles of Beneficial Microorganisms 136 11.4 Conclusion 137 Chapter 12 No Microbes, No Cheese 149Maria Kazou and Effie Tsakalidou 12.1 Cheese for Life: The History 149 12.2 The Technology 150 12.3 The Market 151 12.4 Microbes, Milk, and Cheese: A Long Lasting Threesome Love Affair 151 12.5 Raw Milk Cheese versus Pasteurized Milk Cheese: A Thoughtful Debate about Cheese Quality and Safety 154 12.6 Starter Cultures versus Non-starter Cultures, Alias, Sprinters versus Marathon Runners 155 12.7 Cheese Microbial Communities Thrive while Cheese is Aging and Make a Fortune in Aroma, Flavor, Texture, and Color 156 12.8 Cheese Microbiota and Human Health: Myth or Reality? 157 12.9 Conclusions 158 Chapter 13 The Microbiome of Fermented Sausages 160Ilario Ferrocino, Irene Franciosa, Kalliopi Rantsiou, and Luca S. Cocolin 13.1 Introduction 160 13.2 The Microbiota of Fermented Sausages 161 13.3 The Importance of the Sausage's Mycobiota 164 13.4 Use of the Autochthonous Microbiome to Improve the Quality and Safety of Fermented Sausages 165 13.5 Conclusion 166 Chapter 14 The Sourdough Microbiota and Its Sensory and Nutritional Performances 169Hana Ameur, Kashika Arora, Andrea Polo, and Marco Gobbetti 14.1 Introduction 169 14.2 How the Sourdough Microbiota is Assembled 170 14.2.1 House Microbiota 170 14.2.2 Flour 171 14.2.3 Water 172 14.2.4 Other Ingredients 172 14.3 Where and How to Use the Sourdough 173 14.3.1 Baked Goods and Flours 173 14.3.2 Conditions of Use 173 14.3.3 Microbiological and Biochemical Characteristics 174 14.4 Sourdough to Exploit the Potential of Non-conventional Flours 175 14.4.1 Legumes 175 14.4.2 Pseudo-cereals 177 14.4.3 Milling By-products 177 14.5 The Sensory Performances of Sourdough Baked Goods 178 14.6 The Nutritional Performances of Sourdough Baked Goods 178 14.6.1 Mineral Bioavailability 178 14.6.2 Dietary Fibers 179 14.6.3 Glycemic Index 179 14.6.4 Protein Digestibility 179 14.6.5 Degradation of Anti-nutritional Factors 180 14.7 Conclusions 181 Chapter 15 Beneficial Role of Microorganisms in Olives 185Anthoula A. Argyri and Chrysoula C. Tassou 15.1 Table Olives as Fermented Food 185 15.1.1 Microbiota of Fermented Olives 185 15.1.2 Microbial Starters in Olive Fermentation 186 15.2 Table Olives as Functional/Probiotic Food 186 15.2.1 Probiotic Microorganisms of Olives 187 15.2.2 Probiotic Microorganisms as Starters in Olive Fermentation 191 15.2.2.1 Non-olive Origin Probiotic Starters 191 15.2.2.2 Olive Origin Probiotic Starters 192 15.3 Conclusions 193 Chapter 16 The Functional and Nutritional Aspects of Cocobiota: Lactobacilli 199Jatziri Mota-Gutierrez and Luca S. Cocolin 16.1...